Wilson was head football coach at O. Perry Walker High School in New Orleans, Louisiana from 2001 to 2003. While at O. Perry Walker, Wilson led the Chargers to the 2002 Class 4A state finals. He was honored by the NFL as the 2002 Coach of the Year for the state of Louisiana and was voted as the Louisiana Class 4A Coach of the Year by his fellow coaches. Wilson also was a 2002 Nike National Coach of the Year finalist. During his three years at O. Perry Walker, Wilson had 22 players sign Division I scholarships, including 11 in 2002 to rank as the nation’s largest class of Division I signees by any one high school.[4] He also spent three years as an assistant coach at Edna Karr High Schoolm from 1997 to 2000.

From 2005 to 2007, Wilson was running backs coach at Ole Miss under head coach Ed Orgeron and was a primary character in the book "Meat Market" by Bruce Feldman, which followed Ole Miss through the 2006–07 recruiting season.

Prior to taking the UTSA job, Wilson had been running backs coach and recruiting coordinator at Louisiana State University under head coach Les Miles since 2010.[5] Wilson had also served as the associate head coach for the Tigers.

In 2011, Rivals.com named Wilson the National Recruiter of the Year.[6] In 2014, NFL.com named Wilson the top recruiter in all of college football.[7][8] In 2015, Scout.com honored Wilson as the SEC Recruiter of the Year.[9] In 2015, LSU secured a Top 5 recruiting class, according to 247Sports. The achievement marked the first time since 2002–03 that LSU finished with back-to-back Top 5 recruiting classes in America. From 2011–2014, 29 LSU Tigers have been selected in the NFL Draft which ranks second to Alabama (30).[10]

On January 14, 2016, Wilson was hired as the new head coach of the UTSA Roadrunners. Wilson replaced Larry Coker, who resigned on January 5. Through two seasons, Wilson has lost just as many games as he has won.

Coach Wilson lead UTSA to their first ever bowl game in his first season as coach. Following the season Wilson and his staff secured the #1 ranked recruiting class in C-USA according to the Rivals.com rankings. Wilson's first full class finished 69th in the nation. UTSA had never before finished higher than 103rd prior to this class.